So the problem now is that you have conflicting eggs on your system path that are getting loaded prior to the galaxy supplied eggs.  Galaxy manages its own dependencies, and not relying on those installed via pip/etc.

The simplest, most fool-proof solution here is to use a virtualenv and start galaxy in a clean environment.  See the virtualenv bit here: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer 

Basically, you're going to want to:

pip install virtualenv
virtualenv env_galaxy_clean
source env_galaxy_clean/bin/activate
sh run.sh (or otherwise launch galaxy from within this new environment)


On Wed, Jun 4, 2014 at 10:25 AM, Nikos Sidiropoulos <nikos.sidiro@gmail.com> wrote:

Dannon,

`python scripts/fetch_eggs.py` failed with errors about more packages (pycrypto, poster).

After installing them and running the 'fetch_eggs' script successfully I'm getting this error upon starting the server:

galaxy.eggs ERROR 2014-06-04 16:20:40,694 Dependency "bioblend" requires "simplejson"

Traceback (most recent call last):
  File "./scripts/paster.py", line 33, in <module>
    serve.run()
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run
    invoke(command, command_name, options, args[1:])
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke

    exit_code = runner.run(args)
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run
    result = self.command()
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 643, in command
    app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp
    return loadobj(APP, uri, name=name, **kw)
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 375, in loadobj
    return context.create()
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 813, in create
    return self.object_type.invoke(self)
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 249, in invoke
    return fix_call(context.object, context.global_conf, **context.local_conf)
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call
    val = callable(*args, **kw)
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory
    webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 441, in add_ui_controllers
    module = import_module( module_name )
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py", line 37, in import_module
    __import__(name)
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py", line 20, in <module>
    eggs.require('bioblend')
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py", line 409, in require
    return c[req.project_name].require()
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py", line 237, in require
    dists = self.resolve()
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168, in resolve
    dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch )
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/pkg_resources.py", line 569, in resolve
    raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2 (/steno-internal/projects/galaxy-test/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg), Requirement.parse('simplejson'))

Simplejson is installed in the system and the library folder is in the galaxy user's PYTHONPATH.


On 4 June 2014 15:32, Evan Bollig <boll0107@umn.edu> wrote:
Dannon, 

Do you guys have a web page that documents all of the script/ utilities? I know most of my deployment and upgrade problems have been resolved by various scripts in there, but I have no idea what's available until I turn to this mailing list. 

-E


On Wednesday, June 4, 2014, Dannon Baker <dannon.baker@gmail.com> wrote:
Hey Nikos,

I think you're seeing the same issue from this trello card here: https://trello.com/c/HWuxsftB/1596-fetching-zip-safe-eggs-that-depend-on-other-eggs-will-fail

Can you run `python scripts/fetch_eggs.py` from your galaxy directory?  That should re-fetch galaxy's eggs and you should be up and running again.


On Wed, Jun 4, 2014 at 9:15 AM, Nikos Sidiropoulos <nikos.sidiro@gmail.com> wrote:
Hi all,

after the latest galaxy update I've experienced the following error while trying to start the server.

galaxy.eggs DEBUG 2014-06-04 14:34:56,027 Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
galaxy.eggs ERROR 2014-06-04 14:34:56,047 One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in t
he egg distribution.
galaxy.eggs ERROR 2014-06-04 14:34:56,047 Dependency "bioblend" requires "mock"
Traceback (most recent call last):
  File "./scripts/paster.py", line 33, in <module>
    serve.run()
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run
    invoke(command, command_name, options, args[1:])
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util
/pastescript/serve.py", line 1055, in invoke
    exit_code = runner.run(args)
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run
    result = self.command()
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 643, in command
    app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp
    return loadobj(APP, uri, name=name, **kw)
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 375, in loadobj
    return context.create()
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 813, in create
    return self.object_type.invoke(self)
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 249, in invoke
    return fix_call(context.object, context.global_conf, **context.local_conf)
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call
    val = callable(*args, **kw)
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory
    webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app )
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 441, in add_ui_controllers
    module = import_module( module_name )
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/util/backports/importlib/__init__.py", line 37, in import_module
    __import__(name)
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py", line 20, in <module>
    eggs.require('bioblend')
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py", line 409, in require
    return c[req.project_name].require()
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py", line 237, in require
    dists = self.resolve()
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168, in resolve
    dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch )
  File "/steno-internal/projects/galaxy-test/galaxy-dist/lib/pkg_resources.py", line 569, in resolve
    raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (bioblend 0.4.2 (/steno-internal/projects/galaxy-test/galaxy-dist/eggs/bioblend-0.4.2-py2.7.egg), Requirement.parse('mock'))


First I got and error about the python module 'requests' missing, fixed it using 'pip install', and then got the error above.

Regards,
Nikos

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--
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
evan@msi.umn.edu
boll0107@umn.edu